An ancient and essential miRNA family controls cellular interaction pathways in C. elegans [miRNA-Seq]

The transition from unicellular to multicellular life required the acquisition of coordinated and regulated cellular behaviors, including adhesion and migration. In metazoans, this relies on cell adhesion proteins, signaling systems, and an elaborate extracellular matrix (ECM) that contributes to cell adhesion and to the milieu in which signaling interactions occur. Innovations in these pathways that enabled complex multicellularity occurred at the level of new genes, new functions for existing genes, but also at the regulatory level. Gene regulation by microRNAs expanded with the evolution of multicellularity, but the functions of individual microRNAs in this context are largely unexplored. A single microRNA, miR-100, arose in the last common eumetazoan ancestor and is widely conserved across animals. Here, we reveal the molecular function of the homolog of miR-100 in C. elegans, the miR-51 family. The miR-51 family acts in a dose dependent manner to control morphogenesis by regulating several genes involved in cell signaling, adhesion and migration, including modifiers of the ECM, specifically heparan sulfate sulfotransferases (HSTs). Specific HSTs and signaling pathway components are also predicted conserved targets of miR-100 across vertebrates. Our work suggests that this miRNA provided an innovation in the regulation of cellular interactions early in metazoan evolution, as animals evolved to form more complex bodies. Small RNA sequencing of C. elegans embryos at the comma stage. Embryos of eight different genotypes were sequenced, wildtype (N2) and animals with deletions or mutations in various members of the miR-51 miRNA family. Libraries for all genotypes were prepared in biological duplicates. Spike in oligos were added based on (Lutzmayer et al., 2017, Sci Rep). Protocol details can be found in Dexheimer PJ, Wang J, Cochella L. Two MicroRNAs Are Sufficient for Embryonic Patterning in C. elegans. Curr Biol 2020 Dec 21;30(24):5058-5065.e5. PMID: 33125867